Choco Theme and Updates for WordPress (Cross-Over?)

I am seeing 'updates' for WordPress for the theme I have installed and am using for my Business Website.
After screwing up the CSS and other features, my (excellent) husband cleaned up the mess and adjusted some programming to make it look good.
BUT - I keep getting WordPress 'update' notices and I'm terrified - if I update the WordPress, will that over-wright what programming changes we have made and ensure we have to start over?
Does anyone know the answer to this question?